Epidemiology and risk factors for diarrhoeagenic Escherichia coli carriage among children in northern Ibadan, Nigeria

Abstract

Diarrhea is a leading cause of childhood morbidity in Africa. Outside of multi-country sentinels, of which there are none in Nigeria, few studies focus on bacterial etiology. We performed a case-control study among children under five years of age. Stool specimens were collected from 120 children with, and 357 without, diarrhea attending primary health clinics on the northern outskirts of Ibadan between November 2015 and August 2019. Up to ten E. coli isolates were obtained per specimen and at least three were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes, quality evaluated using QUAST, and Virulencefinder was used to identify virulence genes. The microbiological quality of water from 14 wells within the study area was assessed using total and coliform counts. Diarrhoeagenic Escherichia coli (DEC) were isolated from 79 (65.8%) of cases and 217 (60.8%) control children. All DEC pathotypes except Shiga toxin-producing E. coli, a number of hybrid DEC pathotypes, Salmonella and Yersina spp. were detected but no pathogen showed association with disease (p>0.05). Enterotoxigenic E. coli were more commonly recovered from younger controls but exclusively detected in cases aged over nine months. Temporally-linked, highly similar enteroaggregative E. coli were isolated from children in different households in eight instances. No well water sample drawn in the study qualified as potable. Children in northern Ibadan are commonly colonized with DEC. Access to water and sanitation, and vaccines targeting the most abundant pathogens may be critical for protecting children from the less overt consequences of enteric pathogen carriage.

Insufficiency of PCR diagnostics for Detection of DiarrhoeagenicEscherichia coliin Ibadan, Nigeria

“…Up to ten isolates were obtained per stool specimen and all isolates were subjected to PCR screening. Up to three isolates showing different biochemical and/or Whole genome Sequencing: E. coli genomic DNA were extracted using the Wizard Genomic Extraction kit (Promega) according to the manufacturer's instructions and they were shipped and bulk sequenced in Sanger using the illumina platform as described previously (6). Raw data were assembled by SPAdes assembler and assembly quality was determined using Quality Assessment Tool for Genome Assemblies (QUAST), and CheckM.…”

“…It is common among EAEC strains from some locations, for example the Chile and India strain sets on which that the "EAEC probe" Baudry et al (1990) was validated (50). However subsequent data has shown that CVD432-negative EAEC strains predominate in some geographies, including Nigeria (6,51). The insensitivity of CVD432-based PCR protocols and could be resolved, at least in part by using additional targets as Czeuczulin et al and Boisen et al (52,53) have recommended.…”

“…Unlike EAEC, for which the absence of a precise genetic definition requires multiple targets to be used to identify strains from this pathotype (6,32), ETEC and STEC have genetic definitions based on the presence of toxin genes that encode the virulence factors producing the disease. ETEC are vaccine priority organisms and STEC are reportable.…”

“…Unlike EAEC, for which the absence of a precise genetic definition requires multiple targets to be used to identify strains from this pathotype (6,32) The major advantage of whole genome sequencing is that most DEC pathotypes can be predicted with a high degree of accuracy from sequence data (55). The obvious deterrent for routine use is cost.…”

“…Within each pathotype, there is considerable genetic diversity and different lineages evolved convergently. There are also hybrid strains that carry virulence genes corresponding to multiple pathotypes (2)(3)(4)(5)(6)(7) .…”